X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.h;h=0c6ebe2de76c957f2a3f9c072b9127efb002e5fb;hb=3504e4e2feeb05aabb0c79aa42cb696522030924;hp=6f3455debc4b6f161102a7bd2a75e797d3c639f0;hpb=88fbc534a92cb91900e98a3288dfa1f68828b69b;p=mothur.git

diff --git a/chimeraslayercommand.h b/chimeraslayercommand.h
index 6f3455d..0c6ebe2 100644
--- a/chimeraslayercommand.h
+++ b/chimeraslayercommand.h
@@ -15,6 +15,7 @@
 #include "chimera.h"
 #include "chimeraslayer.h"
 #include "sequenceparser.h"
+#include "sequencecountparser.h"
 
 /***********************************************************/
 
@@ -27,8 +28,10 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "chimera.slayer";		}
 	string getCommandCategory()		{ return "Sequence Processing"; }
+	
 	string getHelpString();	
-	string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. \nhttp://www.mothur.org/wiki/Chimera.slayer"; }
+    string getOutputPattern(string);	
+	string getCitation() { return "Haas BJ, Gevers D, Earl A, Feldgarden M, Ward DV, Giannokous G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methe B, Desantis TZ, Petrosino JF, Knight R, Birren BW (2011). Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res  21:494.\nhttp://www.mothur.org/wiki/Chimera.slayer"; }
 	string getDescription()		{ return "detect chimeric sequences"; }
 	
 	int execute(); 
@@ -50,12 +53,14 @@ private:
 	int divideInHalf(Sequence, string&, string&);
 	map<string, int> sortFastaFile(string, string);
 	map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
+    int sortFastaFile(vector<Sequence>&, map<string, int>&, string newFile);
 	string getNamesFile(string&);
 	//int setupChimera(string,);
 	int MPIExecute(string, string, string, string, map<string, int>&);
-	int deconvoluteResults(SequenceParser*, string, string, string);
+	int deconvoluteResults(map<string, string>&, string, string, string);
 	map<string, int> priority;
 	int setUpForSelfReference(SequenceParser*&, map<string, string>&, map<string, map<string, int> >&, int);
+    int setUpForSelfReference(SequenceCountParser*&, map<string, string>&, map<string, map<string, int> >&, int);
 	int driverGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
 	int createProcessesGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
 	int MPIExecuteGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
@@ -65,8 +70,8 @@ private:
 	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
 	#endif
 
-	bool abort, realign, trim, trimera, save;
-	string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
+	bool abort, realign, trim, trimera, save, hasName, hasCount, dups;
+	string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
 	int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
 	float divR;
 	
@@ -172,7 +177,7 @@ struct slayerData {
 };
 
 /**************************************************************************************************/
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 static DWORD WINAPI MySlayerThreadFunction(LPVOID lpParam){ 
 	slayerData* pDataArray;